Despite the fact that the genus Myotis (Mouse-Eared bats) isone of the most investigated microchiropteran groups, recent molecularstudies highlighted the presence of several cryptic species with substantialimplications for ecological and conservation issues. Our dataset includes 55coxI sequences from 11 morphologically-identified Italian Mouse-Eared batsspecies. We applied an integrated approach comparing data from a traditionalmorphological identification and molecular variability in a fragment of themitochondrial coxI gene (DNA barcoding). Our results clearly show a strongcoherence between the two identification approaches for almost all of theexamined species, and revealed interesting patterns of intraspecific variabilitywithin the species M. nattereri. Finally, we successfully tested the efficacy ofour identification method on undetermined individuals sampled in the field.